@Matt Dillon , From your description, it seems you use Autopilot Hybrid Azure AD enrollment and co-management. In Fact, there are two enrollment methods. You can choose one of them to do the enrollment.
https://learn.microsoft.com/en-us/mem/intune/enrollment/device-enrollment#windows-enrollment-methods
For co-management, there are two paths to do the enrollment. One is for existing Configuration Manager device. The other is for Internet device with first enrolled into Intune. Here is a link with more details for your reference:
https://learn.microsoft.com/en-us/mem/configmgr/comanage/quickstart-paths
Based on my research, there is a new technology to put Autopilot into co-management. But currently, Hybrid Azure AD-joined devices is not supported.
https://learn.microsoft.com/en-us/managed-desktop/get-started/autopilot-co-management
Meanwhile, I notice you want to know if BitLocker can enable during Autopilot enrollment. During Windows Autopilot Enrollment Status page, it will install some applications and applied some profiles.
https://learn.microsoft.com/en-us/mem/autopilot/enrollment-status
For BitLocker, in Windows 10 1809 and above, it will wait to begin encrypting until the end of OOBE, after the ESP device configuration phase has completed. Here is a link with more details:
https://oofhours.com/2019/08/26/bitlocker-esp-and-windows-autopilot-working-in-harmony/
Note: Non-Microsoft link, just for your reference.
To enable BitLocker for windows device with Microsoft Intune, we can configure "Endpoint security disk encryption policy" or "Device configuration profile for endpoint protection". Here is a link with more details for your reference:
https://learn.microsoft.com/en-us/mem/intune/protect/encrypt-devices
For your scenario, I suggest choosing only one method to do the enrollment to avoid any issue. Then try to deploy BitLocker policy via Intune. Check the policy to see if is applied to the device successfully. If not, we can follow the following links to do the troubleshooting:
https://learn.microsoft.com/en-us/troubleshoot/mem/intune/troubleshoot-bitlocker-policies
https://techcommunity.microsoft.com/t5/intune-customer-success/support-tip-troubleshooting-bitlocker-policies-in-microsoft/ba-p/863670
Hope it can help.
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